Variant report

Variant	rs515064
Chromosome Location	chr1:70904068-70904069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70902352..70904589-chr1:70911480..70913047,2	K562	blood:
2	chr1:70900549..70904581-chr1:70906967..70911006,5	K562	blood:
3	chr1:70878824..70881393-chr1:70902317..70904279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271992	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1145919	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4650049	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs473334	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs525919	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs535112	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577476	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs663649	0.91[CEU][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs672203	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828355	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv461828	chr1:70880717-70922360	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv546456	chr1:70880717-70922360	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs515064	LRRC40	cis	cerebellum	SCAN
rs515064	SRSF11	cis	cerebellum	SCAN
rs515064	LRRIQ3	cis	parietal	SCAN
rs515064	CTH	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70877400-70906400	Weak transcription	Small Intestine	intestine
2	chr1:70877400-70906600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:70877800-70907800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:70878000-70908200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:70878200-70907000	Weak transcription	Psoas Muscle	Psoas
6	chr1:70878200-70909600	Weak transcription	Gastric	stomach
7	chr1:70878400-70907000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:70878600-70906000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:70884400-70909000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:70886400-70906600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:70886400-70906800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:70888000-70906000	Weak transcription	Fetal Brain Male	brain
13	chr1:70891400-70907400	Weak transcription	Fetal Stomach	stomach
14	chr1:70892200-70907400	Weak transcription	Fetal Brain Female	brain
15	chr1:70892400-70906400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:70892600-70906200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:70893200-70907800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:70894000-70906200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:70894400-70906600	Weak transcription	Fetal Heart	heart
20	chr1:70894600-70905200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:70895400-70905600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:70895400-70906200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:70895400-70907000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:70895600-70905400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:70895800-70912000	Weak transcription	Hela-S3	cervix
26	chr1:70896000-70905400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:70896000-70905800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:70896400-70904400	Weak transcription	HSMM	muscle
29	chr1:70896400-70905000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:70896600-70905800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:70896800-70905000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:70897000-70909600	Weak transcription	Pancreas	Pancrea
33	chr1:70897600-70904600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:70898000-70907800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:70898200-70904400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:70898200-70906200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:70898200-70907400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:70898200-70908600	Strong transcription	Liver	Liver
39	chr1:70898400-70908000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:70899400-70904600	Weak transcription	Right Ventricle	heart
41	chr1:70899600-70906200	Weak transcription	GM12878-XiMat	blood
42	chr1:70899600-70906600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:70899600-70906800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:70899600-70908000	Weak transcription	Brain Germinal Matrix	brain
45	chr1:70900000-70905200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:70900000-70906400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:70900000-70906600	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:70900000-70906800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:70900000-70907800	Weak transcription	Brain Angular Gyrus	brain
50	chr1:70900200-70906400	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links